To explore the spatial and temporal distribution characteristics of phytoplankton functional groups (PFGs) of the Dongta spawning grounds in the Pearl River, China, quarterly surveys of this area were carried out during March, 2016 to December, 2018, and the ecological status was analyzed and evaluated according to PFGs assemblage index (Q index). 26 PFGs were identified, and the dominant PFGs were C, D, J, K, L-0, MP, N, P, S1, S2, T, W1, W2, X2, Y in this area. Phytoplankton Q indexes varied from 1.83 to 3.73, with the mean value 2.91, which showed that the ecological status of the Dongta spawning grounds was "medium" and "good", but parts occasionally were "tolerable". Temporally, the general ecological status was good in March and June, but it was medium in September and December. Basing on our study, the results showed that: (1) factors including water velocity (V), DO, Chla, phosphate, oxidation reduction potential, total phosphorus, electrical conductivity, total dissolved solid and salinity were significantly correlated with the dominant PFGs; (2) the phytoplankton Q index was significantly correlated with the V. It was suggested that after the construction and operation of Datengxia Water Dam and its upper reaches cascade dams, attention should be paid to regulate the water flow and velocity in the lower reaches of the river by means of ecological operation, so as to ensure the functions of the spawning grounds and protect the fishery conservation zones in the mainstream of the Pearl River.